Variant report

Variant	rs1650954
Chromosome Location	chr19:53488868-53488869
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53482347..53484833-chr19:53488292..53490832,2	K562	blood:

Variant related genes	Relation type
ENSG00000242779	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11084213	1.00[ASN][1000 genomes]
rs11672193	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11672195	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1583963	0.86[ASN][1000 genomes]
rs57124053	0.85[ASN][1000 genomes]
rs57907732	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59870789	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60058476	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7251099	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257730	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv432072	chr19:53144788-53554388	Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1058903	chr19:53193570-53489633	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1067280	chr19:53193570-53567287	Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv544062	chr19:53193570-53567287	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv580030	chr19:53194344-53547394	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
11	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
12	esv2757701	chr19:53470514-53554240	Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	esv34546	chr19:53478109-53509688	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv817861	chr19:53484032-53505860	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv458753	chr19:53485090-53552296	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv458754	chr19:53485090-53552296	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv580046	chr19:53485090-53552296	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53467000-53489000	Weak transcription	Right Ventricle	heart
2	chr19:53467000-53494600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr19:53467200-53489200	Weak transcription	Colon Smooth Muscle	Colon
4	chr19:53467200-53495400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:53472600-53489000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:53472800-53495800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr19:53473000-53489400	Weak transcription	Brain Anterior Caudate	brain
8	chr19:53473600-53495800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:53474000-53495800	Weak transcription	Fetal Lung	lung
10	chr19:53481200-53495400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr19:53482000-53489800	Weak transcription	NHLF	lung
12	chr19:53482000-53491200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr19:53485400-53490600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:53487200-53489000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:53487200-53490800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:53487400-53490800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:53487400-53492800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr19:53487600-53489200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:53487600-53489400	ZNF genes & repeats	Fetal Intestine Large	intestine
20	chr19:53487600-53489800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:53487600-53489800	ZNF genes & repeats	Ovary	ovary
22	chr19:53487600-53490200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:53487600-53490800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:53487600-53490800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
25	chr19:53487600-53491000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
26	chr19:53487600-53491200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:53487600-53492600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
28	chr19:53487600-53493200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr19:53487800-53489000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr19:53487800-53489800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:53487800-53489800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:53487800-53490000	ZNF genes & repeats	Adipose Nuclei	Adipose
33	chr19:53487800-53490600	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr19:53487800-53490800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:53487800-53490800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:53487800-53491000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr19:53488000-53489000	ZNF genes & repeats	K562	blood
38	chr19:53488000-53489400	Weak transcription	Osteobl	bone
39	chr19:53488000-53489800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
40	chr19:53488000-53490000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:53488000-53490800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:53488000-53490800	ZNF genes & repeats	Liver	Liver
43	chr19:53488000-53490800	ZNF genes & repeats	HUVEC	blood vessel
44	chr19:53488200-53489000	Weak transcription	Gastric	stomach
45	chr19:53488200-53490200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
46	chr19:53488200-53491000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
47	chr19:53488200-53491800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
48	chr19:53488200-53493200	Strong transcription	Placenta	Placenta
49	chr19:53488200-53495800	Weak transcription	Brain Hippocampus Middle	brain
50	chr19:53488400-53489200	Strong transcription	Primary T killer memory cells from peripheral blood	blood

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